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- EMDB-66506: Phage T4 inner baseplate in post-tail-contraction state (genome-f... -

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Basic information

Entry
Database: EMDB / ID: EMD-66506
TitlePhage T4 inner baseplate in post-tail-contraction state (genome-full particle)
Map data
Sample
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Baseplate wedge protein gp6
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate wedge protein gp25
    • Protein or peptide: Baseplate wedge protein gp53
    • Protein or peptide: Tail tube protein gp19
KeywordsBacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / viral tail assembly / structural molecule activity / identical protein binding
Similarity search - Function
Baseplate wedge protein gp53, bacteriophage T4 / Base plate wedge protein 53 / Baseplate wedge protein gp7 / : / : / : / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp6 ...Baseplate wedge protein gp53, bacteriophage T4 / Base plate wedge protein 53 / Baseplate wedge protein gp7 / : / : / : / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp6 / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / IraD/Gp25-like / Baseplate wedge protein gp25 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate wedge protein gp25 / Tail tube protein gp19 / Baseplate wedge protein gp53 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShao Q / Dong J / Wang A / Hu H / Yue J / Li H / Li Y / Zhang Q / Liu J / Sun L ...Shao Q / Dong J / Wang A / Hu H / Yue J / Li H / Li Y / Zhang Q / Liu J / Sun L / Fokine A / Rao VB / Tao P / Fang Q
Funding support China, United States, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371285 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175340 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DP1DA060580 United States
National Science Foundation (NSF, United States)MCB-0923873 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110243 United States
National Institutes of Health/Office of the Director1S10OD023603-01A1 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Cryo-EM Structures of Phage T4 Infection Intermediate.
Authors: Qianqian Shao / Junhua Dong / Aohan Wang / Hongli Hu / Jian Yue / Hongmei Li / Yinyin Li / Qinfen Zhang / Jun Liu / Lei Sun / Andrei Fokine / Venigalla B Rao / Pan Tao / Qianglin Fang /
Abstract: Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. ...Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. Here, we capture a pre-genome-release intermediate of myophage T4 and determine its structure by cryo-electron microscopy. Comparative analysis of this tail-contracted, pre-genome-release intermediate structure with the mature T4 virion and the tail-contracted, post-genome-release structure reveals structural transitions in the tail, tape-measure protein (TMP), baseplate, and long tail fibers that drive genome delivery. Our findings further suggest that tail sheath contraction is coupled to a coordinated repositioning of the viral DNA-TMP complex, potentially facilitating genome translocation via charge-mediated interactions. It appears that the expelled TMP may further reorganize into a putative transmembrane complex that supports genome delivery into the host cytosol.
History
DepositionOct 9, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66506.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 560 pix.
= 917.28 Å		1.64 Å/pix.
x 560 pix.
= 917.28 Å		1.64 Å/pix.
x 560 pix.
= 917.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.07225352 - 0.13439658
Average (Standard dev.)-0.00003827217 (±0.005613607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 917.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66506_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66506_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66506_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage T4

EntireName: Escherichia phage T4 (virus)
Components
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Baseplate wedge protein gp6
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate wedge protein gp25
    • Protein or peptide: Baseplate wedge protein gp53
    • Protein or peptide: Tail tube protein gp19

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Supramolecule #1: Escherichia phage T4

SupramoleculeName: Escherichia phage T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681598 / Sci species name: Escherichia phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Baseplate wedge protein gp6

MacromoleculeName: Baseplate wedge protein gp6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 74.492641 KDa
SequenceString: MANTPVNYQL TRTANAIPEI FVGGTFAEIK QNLIEWLNGQ NEFLDYDFEG SRLNVLCDLL AYNTLYIQQF GNAAVYESFM RTANLRSSV VQAAQDNGYL PTSKSAAQTE IMLTCTDALN RNYITIPRGT RFLAYAKDTS VNPYNFVSRE DVIAIRDKNN Q YFPRLKLA ...String:
MANTPVNYQL TRTANAIPEI FVGGTFAEIK QNLIEWLNGQ NEFLDYDFEG SRLNVLCDLL AYNTLYIQQF GNAAVYESFM RTANLRSSV VQAAQDNGYL PTSKSAAQTE IMLTCTDALN RNYITIPRGT RFLAYAKDTS VNPYNFVSRE DVIAIRDKNN Q YFPRLKLA QGRIVRTEII YDKLTPIIIY DKNIDRNQVK LYVDGAEWIN WTRKSMVHAG STSTIYYMRE TIDGNTEFYF GE GEISVNA SEGALTANYI GGLKPTQNST IVIEYISTNG ADANGAVGFS YADTLTNITV ININENPNDD PDFVGADGGG DPE DIERIR ELGTIKRETQ QRCVTATDYD TFVSERFGSI IQAVQTFTDS TKPGYAFIAA KPKSGLYLTT VQREDIKNYL KDYN LAPIT PSIISPNYLF IKTNLKVTYA LNKLQESEQW LEGQIIDKID RYYTEDVEIF NSSFAKSKML TYVDDADHSV IGSSA TIQM VREVQNFYKT PEAGIKYNNQ IKDRSMESNT FSFNSGRKVV NPDTGLEEDV LYDVRIVSTD RDSKGIGKVI IGPFAS GDV TENENIQPYT GNDFNKLANS DGRDKYYVIG EINYPADVIY WNIAKINLTS EKFEVQTIEL YSDPTDDVIF TRDGSLI VF ENDLRPQYLT IDLEPISQ

UniProtKB: Baseplate wedge protein gp6

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Macromolecule #2: Baseplate wedge protein gp7

MacromoleculeName: Baseplate wedge protein gp7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 119.336516 KDa
SequenceString: MTVKAPSVTS LRISKLSANQ VQVRWDDVGA NFYYFVEIAE TKTNSGENLP SNQYRWINLG YTANNSFFFD DADPLTTYII RVATAAQDF EQSDWIYTEE FETFATNAYT FQNMIEMQLA NKFIQEKFTL NNSDYVNFNN DTIMAALMNE SFQFSPSYVD V SSISNFII ...String:
MTVKAPSVTS LRISKLSANQ VQVRWDDVGA NFYYFVEIAE TKTNSGENLP SNQYRWINLG YTANNSFFFD DADPLTTYII RVATAAQDF EQSDWIYTEE FETFATNAYT FQNMIEMQLA NKFIQEKFTL NNSDYVNFNN DTIMAALMNE SFQFSPSYVD V SSISNFII GENEYHEIQG SIQQVCKDIN RVYLMESEGI LYLFERYQPV VKVSNDKGQT WKAVKLFNDR VGYPLSKTVY YQ SANTTYV LGYDKIFYGR KSTDVRWSAD DVRFSSQDIT FAKLGDQLHL GFDVEIFATY ATLPANVYRI AEAITCTDDY IYV VARDKV RYIKTSNALI DFDPLSPTYS ERLFEPDTMT ITGNPKAVCY KMDSICDKVF ALIIGEVETL NANPRTSKII DSAD KGIYV LNHDEKTWKR VFGNTEEERR RIQPGYANMS TDGKLVSLSS SNFKFLSDNV VNDPETAAKY QLIGAVKYEF PREWL ADKH YHMMAFIADE TSDWETFTPQ PMKYYAEPFF NWSKKSNTRC WINNSDRAVV VYADLKYTKV IENIPETSPD RLVHEY WDD GDCTIVMPNV KFTGFKKYAS GMLFYKASGE IISYYDFNYR VRDTVEIIWK PTEVFLKAFL QNQEHETPWS PEEERGL AD PDLRPLIGTM MPDSYLLQDS NFEAFCEAYI QYLSDGYGTQ YNNLRNLIRN QYPREEHAWE YLWSEIYKRN IYLNADKR D AVARFFESRS YDFYSTKGIE ASYKFLFKVL YNEEVEIEIE SGAGTEYDII VQSDSLTEDL VGQTIYTATG RCNVTYIER SYSNGKLQWT VTIHNLLGRL IAGQEVKAER LPSFEGEIIR GVKGKDLLQN NIDYINRSRS YYVMKIKSNL PSSRWKSDVI RFVHPVGFG FIAITLLTMF INVGLTLKHT ETIINKYKNY KWDSGLPTEY ADRIAKLTPT GEIEHDSVTG EAIYEPGPMA G VKYPLPDD YNAENNNSIF QGQLPSERRK LMSPLFDASG TTFAQFRDLV NKRLKDNIGN PRDPENPTQV KIDE

UniProtKB: Baseplate wedge protein gp7

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Macromolecule #3: Baseplate wedge protein gp25

MacromoleculeName: Baseplate wedge protein gp25 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 15.111101 KDa
SequenceString:
MANINKLYSD IDPEMKMDWN KDVSRSLGLR SIKNSLLGII TTRKGSRPFD PEFGCDLSDQ LFENMTPLTA DTVERNIESA VRNYEPRID KLAVNVIPVY DDYTLIVEIR FSVIDNPDDI EQIKLQLASS NRV

UniProtKB: Baseplate wedge protein gp25

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Macromolecule #4: Baseplate wedge protein gp53

MacromoleculeName: Baseplate wedge protein gp53 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 22.990885 KDa
SequenceString: MLFTFFDPIE YAAKTVNKNA PTIPMTDIFR NYKDYFKRAL AGYRLRTYYI KGSPRPEELA NAIYGNPQLY WVLLMCNDNY DPYYGWITS QEAAYQASIQ KYKNVGGDQI VYHVNENGEK FYNLISYDDN PYVWYDKGDK ARKYPQYEGA LAAVDTYEAA V LENEKLRQ ...String:
MLFTFFDPIE YAAKTVNKNA PTIPMTDIFR NYKDYFKRAL AGYRLRTYYI KGSPRPEELA NAIYGNPQLY WVLLMCNDNY DPYYGWITS QEAAYQASIQ KYKNVGGDQI VYHVNENGEK FYNLISYDDN PYVWYDKGDK ARKYPQYEGA LAAVDTYEAA V LENEKLRQ IKIIAKSDIN SFMNDLIRIM EKSYGNDK

UniProtKB: Baseplate wedge protein gp53

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Macromolecule #5: Tail tube protein gp19

MacromoleculeName: Tail tube protein gp19 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 18.479613 KDa
SequenceString:
MFVDDVTRAF ESGDFARPNL FQVEISYLGQ NFTFQCKATA LPAGIVEKIP VGFMNRKINV AGDRTFDDWT VTVMNDEAHD ARQKFVDWQ SIAAGQGNEI TGGKPAEYKK SAIVRQYARD AKTVTKEIEI KGLWPTNVGE LQLDWDSNNE IQTFEVTLAL D YWE

UniProtKB: Tail tube protein gp19

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Number real images: 2276 / #0 - Average exposure time: 8.0 sec. / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number real images: 5090 / #1 - Average exposure time: 8.0 sec. / #1 - Average electron dose: 59.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 116671
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 40108
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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